Plotting the colors with the positive and negative correlations.

[Aristotle1992]

#for root samples root_bac_sub_no_bad_Filtered_final_non_normalized <- readRDS(file = "C:/Microbiome/RDS/root_bac_sub_no_bad_Filtered_final_non_normalized.rds")

root_norm = transform_sample_counts(root_bac_sub_no_bad_Filtered_final_non_normalized, function(x) x / sum(x) ) root_network = filter_taxa(root_norm, function(x) mean(x) > 0.0001, TRUE) root_network

#first convert to microtable root_amp <- phyloseq2meco(root_network) root_amp

The parameter cor_method in trans_network is used to select correlation calculation method.

default pearson or spearman correlation invoke R base cor.test, a little slow

#net_root <- trans_network$new(dataset = root_amp, cor_method = "spearman", filter_thres = 0.001)

return net_root$res_cor_p list, containing two tables: correlation coefficient table and p value table

require WGCNA package

if(!require("WGCNA")) install.packages("WGCNA", repos = BiocManager::repositories()) net_root <- trans_network$new(dataset = root_amp, cor_method = "spearman", use_WGCNA_pearson_spearman = TRUE, filter_thres = 0.0001)

write.csv(t1[["res_cor_p"]][["p"]], "C:/Microbiome/network files/root_cor.csv")

use arbitrary coefficient threshold to contruct network

net_root$cal_network(COR_p_thres = 0.05, COR_cut = 0.6, COR_p_adjust = "fdr")

return net_root$res_network

invoke igraph cluster_fast_greedy function for this undirected network

net_root$cal_module(method = "cluster_fast_greedy")

require rgexf package to be installed

net_root$save_network(filepath = "C:/Microbiome/network files/root_network.gexf")

My next goal is to plot the colors with the positive and negative correlations using gephi and my problem is how do I add the correlation matrix to the gephi file format as they are in matrix. In essence i want my network plot to show just the negative and positive correlations between the phylum. Thanks

[ChiLiubio]

Hi. The positive and negative labels (+ and -) have been added into the network. When you open the saved root_network.gexf, please try to find it following those steps: Click Overview -> Appearance (in top left cornor) -> Edges -> Partition -> Select label. That is it.

[Aristotle1992]

Thanks so much for your reply but when i followed the step you stated i only found + and no -. What could be a likely cause?

[ChiLiubio]

The reason should be that there is no negative significant correlation after the filtering with your parameters. To test this, you can lower the correlation coefficient threshold and try again.

[Aristotle1992]

oh ok thanks. I will try that out.